On Mon, Sep 12, 2011 at 8:10 AM, Guenegou, Guillaume [JRDFR] <
GGUENEGO.its.jnj.com> wrote:
> Dear all,
>
>
>
> Versions : Amber11/AmberTools 1.5
>
>
>
> I use sleap in order to convert a mol2 file into a sdf file.
>
>
>
> My input file looks like this :
>
> source leaprc.ff03.r1
>
> source leaprc.gaff
>
> molecule = loadmol2 molecule.mol2
>
> savesdf molecule molecule.sdf
>
> quit
>
>
>
> My mol2 file contains aromatic bonds. But, surprise, the sdf file does
> not contain anymore aromatic bonds.
>
> I tried several viewers and the problem remains. Double bonds are still
> there but aromatic bonds became single bond.
>
>
>
> Is this a bug or is there anything I am doing wrong?
>
Amber doesn't typically retain "detailed" bond information like bond
orders. It makes no use of them anywhere in the simulation programs (the
only place they're used/guessed is for antechamber when they're trying to
determine bonded parameters.
If you're looking for programs that will retain this bonding information,
you'll probably have to look elsewhere. If you're trying to prepare an
amber topology file, then this bonding information is completely
unnecessary.
It could also be the visualization program you're using that's filling in
the bonds as necessary...
HTH,
Jason
>
>
> G.GUENEGOU
>
>
>
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Sep 12 2011 - 06:00:04 PDT
